"I think Hurricane Neddy is much worse than the Fake Skinner episode"
Can't agree w/ this. The depiction of Skinner as a reformed delinquent never rings true whereas the explanation of Ned's behavior actually added dimension to the character, rather than him just being yet another Jesus freak. Both scenarios/episodes are admittedly pretty gimmicky but in addition to my previous points, I'd also say that "Hurricane Neddy" simply makes me laugh more. And I don't think either episode really "ruins" the characters. I might feel differently if there were constant references to Skinner's identity or, even worse, if Ned had actually delivered on his promise and stopped bottling up his anger in the episodes that followed but that never happened (though I wouldn't be surprised if they did that shit in recent seasons)
As Matt has pointed out, the main case of them ruining a classic character is Mr. Burns. During the show's peak, he was arguably one of the best characters- consistently hilarious, endearingly bizarre and above all, he actually registered as being pure evil. But as early as season 10 or 11 or so (though it probably gradually started happening in earlier seasons), they started just making him a cute and cuddly old eccentric so whenever they had him do anything evil, it always seemed contrived